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- PDB-1sgl: The three-dimensional structure and X-ray sequence reveal that tr... -

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Basic information

Entry
Database: PDB / ID: 1sgl
TitleThe three-dimensional structure and X-ray sequence reveal that trichomaglin is a novel S-like ribonuclease
Componentstrichomaglin
KeywordsHYDROLASE / trichomaglin / S-like ribonuclease / X-ray sequence / mass spectroscopic analysis
Function / homology
Function and homology information


ribonuclease T2 activity / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Ribonuclease T2, eukaryotic / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrichosanthes lepiniana (plant)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsGan, J.-H. / Yu, L. / Wu, J. / Xu, H. / Choudhary, J.S. / Blackstock, W.P. / Liu, W.-Y. / Xia, Z.-X.
CitationJournal: Structure / Year: 2004
Title: The three-dimensional structure and X-ray sequence reveal that trichomaglin is a novel S-like ribonuclease.
Authors: Gan, J.H. / Yu, L. / Wu, J. / Xu, H. / Choudhary, J.S. / Blackstock, W.P. / Liu, W.Y. / Xia, Z.X.
History
DepositionFeb 24, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: trichomaglin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9375
Polymers23,5531
Non-polymers3844
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.990, 93.990, 57.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein trichomaglin / S-like ribonuclease


Mass: 23552.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichosanthes lepiniana (plant) / Organ: root tuber
References: UniProt: P84146, UniProt: E0CX00*PLUS, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, tris-hydrochloric acid, potassium hydrogen sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→23.56 Å / Num. all: 14893 / Num. obs: 14868 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.1 / Net I/σ(I): 4609.6
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 575.1 / Num. unique all: 982 / Rsym value: 0.662 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→23.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 446341.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1459 10.1 %RANDOM
Rwork0.199 ---
all0.203 14376 --
obs0.199 14376 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8823 Å2 / ksol: 0.338695 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0.31 Å20 Å2
2---1.39 Å20 Å2
3---2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 20 62 1701
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 118 8.7 %
Rwork0.254 1231 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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